HEADER OXIDOREDUCTASE 02-DEC-15 5FPL TITLE CRYSTAL STRUCTURE OF HUMAN JARID1B IN COMPLEX WITH CCT363901 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 5B, LYSINE-SPECIFIC DEMETHYLASE COMPND 3 5B; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: JMJC DOMAIN, RESIDUES 25-101,374-772; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PFB-LIC-BSE KEYWDS OXIDOREDUCTASE, LYSINE-SPECIFIC DEMETHYLASE 5B EXPDTA X-RAY DIFFRACTION AUTHOR V.SRIKANNATHASAN,L.B.YANN-VAI,R.NOWAK,C.JOHANSSON,C.GILEADI,F.VON AUTHOR 2 DELFT,C.H.ARROWSMITH,C.BOUNTRA,A.EDWARDS,P.BRENNAN,K.HUBER, AUTHOR 3 U.OPPERMANN REVDAT 6 20-NOV-24 5FPL 1 REMARK REVDAT 5 10-JAN-24 5FPL 1 REMARK LINK REVDAT 4 24-JAN-18 5FPL 1 JRNL REVDAT 3 14-DEC-16 5FPL 1 AUTHOR REVDAT 2 09-MAR-16 5FPL 1 JRNL REVDAT 1 20-JAN-16 5FPL 0 JRNL AUTH V.BAVETSIAS,R.M.LANIGAN,G.F.RUDA,B.ATRASH,M.G.MCLAUGHLIN, JRNL AUTH 2 A.TUMBER,N.Y.MOK,Y.LE BIHAN,S.DEMPSTER,K.J.BOXALL, JRNL AUTH 3 F.JEGANATHAN,S.B.HATCH,P.SAVITSKY,S.VELUPILLAI,T.KROJER, JRNL AUTH 4 K.S.ENGLAND,J.SEJBERG,C.THAI,A.DONOVAN,A.PAL,G.SCOZZAFAVA, JRNL AUTH 5 J.M.BENNETT,A.KAWAMURA,C.JOHANSSON,A.SZYKOWSKA,C.GILEADI, JRNL AUTH 6 N.A.BURGESS-BROWN,F.VON DELFT,U.OPPERMANN,Z.WALTERS, JRNL AUTH 7 J.SHIPLEY,F.I.RAYNAUD,S.M.WESTAWAY,R.K.PRINJHA,O.FEDOROV, JRNL AUTH 8 R.BURKE,C.J.SCHOFIELD,I.M.WESTWOOD,C.BOUNTRA,S.MULLER, JRNL AUTH 9 R.L.M.VAN MONTFORT,P.E.BRENNAN,J.BLAGG JRNL TITL 8-SUBSTITUTED PYRIDO[3,4-D]PYRIMIDIN-4(3H)-ONE DERIVATIVES JRNL TITL 2 AS POTENT, CELL PERMEABLE, KDM4 (JMJD2) AND KDM5 (JARID1) JRNL TITL 3 HISTONE LYSINE DEMETHYLASE INHIBITORS. JRNL REF J.MED.CHEM. V. 59 1388 2016 JRNL REFN ISSN 0022-2623 JRNL PMID 26741168 JRNL DOI 10.1021/ACS.JMEDCHEM.5B01635 REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.2 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.17 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 38565 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 1949 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 19 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.35 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.41 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.93 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2957 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2414 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2814 REMARK 3 BIN R VALUE (WORKING SET) : 0.2393 REMARK 3 BIN FREE R VALUE : 0.2839 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.84 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 143 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3644 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 279 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 65.42 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 65.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.04030 REMARK 3 B22 (A**2) : 0.04030 REMARK 3 B33 (A**2) : -0.08070 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.286 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.203 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.162 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.190 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.158 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.943 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 3881 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 5289 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1298 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 89 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 588 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 3881 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 3 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 486 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : 9 ; 1.000 ; HARMONIC REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 4494 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.07 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.25 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 17.79 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: {A|25 - 375} REMARK 3 ORIGIN FOR THE GROUP (A): 87.7146 70.9559 17.8285 REMARK 3 T TENSOR REMARK 3 T11: -0.2428 T22: 0.1637 REMARK 3 T33: -0.1092 T12: -0.1880 REMARK 3 T13: 0.0198 T23: -0.0692 REMARK 3 L TENSOR REMARK 3 L11: 2.5556 L22: 1.4576 REMARK 3 L33: 3.0510 L12: 0.2162 REMARK 3 L13: -0.1350 L23: -0.2293 REMARK 3 S TENSOR REMARK 3 S11: 0.0580 S12: -0.2087 S13: 0.1129 REMARK 3 S21: 0.0106 S22: -0.1624 S23: -0.0173 REMARK 3 S31: 0.1464 S32: -0.2742 S33: 0.1044 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: {A|376 - 594} REMARK 3 ORIGIN FOR THE GROUP (A): 88.1217 66.3227 13.9997 REMARK 3 T TENSOR REMARK 3 T11: -0.2251 T22: 0.1493 REMARK 3 T33: -0.1377 T12: -0.1832 REMARK 3 T13: 0.0516 T23: -0.0342 REMARK 3 L TENSOR REMARK 3 L11: 1.9647 L22: 1.0033 REMARK 3 L33: 2.6633 L12: -0.0677 REMARK 3 L13: 0.4017 L23: -0.3590 REMARK 3 S TENSOR REMARK 3 S11: 0.0089 S12: -0.0605 S13: 0.0009 REMARK 3 S21: -0.0595 S22: -0.0528 S23: 0.0058 REMARK 3 S31: 0.3528 S32: -0.3647 S33: 0.0439 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: {A|595 - 754} REMARK 3 ORIGIN FOR THE GROUP (A): 57.4338 64.6960 6.2049 REMARK 3 T TENSOR REMARK 3 T11: -0.2178 T22: 0.1522 REMARK 3 T33: -0.0594 T12: -0.0164 REMARK 3 T13: 0.0033 T23: -0.0586 REMARK 3 L TENSOR REMARK 3 L11: 2.7385 L22: 0.6363 REMARK 3 L33: 1.2273 L12: 0.5237 REMARK 3 L13: 0.5532 L23: -0.7238 REMARK 3 S TENSOR REMARK 3 S11: -0.1331 S12: 0.4321 S13: 0.1541 REMARK 3 S21: -0.1481 S22: 0.2486 S23: 0.1400 REMARK 3 S31: -0.1250 S32: 0.2229 S33: -0.1155 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5FPL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-DEC-15. REMARK 100 THE DEPOSITION ID IS D_1290065692. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUL-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38565 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 46.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 20.10 REMARK 200 R MERGE (I) : 0.15000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.2700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 19.70 REMARK 200 R MERGE FOR SHELL (I) : 0.15000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 14.27 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 5A1F REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 8.0, 0.8M POTASSIUM REMARK 280 PHOSPHATE-DIBASIC, 0.8M SODIUM PHOSPHATE MONOBASIC REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 101.40000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 50.70000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 76.05000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 25.35000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 126.75000 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 101.40000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 50.70000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 25.35000 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 76.05000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 126.75000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 LEU A 101 REMARK 465 GLY A 102 REMARK 465 GLY A 103 REMARK 465 GLY A 104 REMARK 465 GLY A 105 REMARK 465 LYS A 444 REMARK 465 TYR A 755 REMARK 465 ASN A 756 REMARK 465 GLU A 757 REMARK 465 TRP A 758 REMARK 465 ALA A 759 REMARK 465 LEU A 760 REMARK 465 ASN A 761 REMARK 465 VAL A 762 REMARK 465 ASN A 763 REMARK 465 GLU A 764 REMARK 465 ALA A 765 REMARK 465 LEU A 766 REMARK 465 GLU A 767 REMARK 465 ALA A 768 REMARK 465 LYS A 769 REMARK 465 ILE A 770 REMARK 465 ASN A 771 REMARK 465 LYS A 772 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 40 CG CD OE1 OE2 REMARK 470 LYS A 51 CD CE NZ REMARK 470 LYS A 100 NZ REMARK 470 LYS A 408 CE NZ REMARK 470 SER A 431 OG REMARK 470 LYS A 432 CD CE NZ REMARK 470 GLU A 433 CG CD OE1 OE2 REMARK 470 LYS A 446 NZ REMARK 470 ASP A 478 CG OD1 OD2 REMARK 470 LYS A 483 CD CE NZ REMARK 470 LYS A 535 CD CE NZ REMARK 470 LYS A 536 CD CE NZ REMARK 470 LYS A 540 CE NZ REMARK 470 SER A 544 OG REMARK 470 LEU A 548 CD1 REMARK 470 LEU A 549 CG CD1 CD2 REMARK 470 LEU A 620 CD1 CD2 REMARK 470 LYS A 639 NZ REMARK 470 LYS A 653 CE NZ REMARK 470 LYS A 671 NZ REMARK 470 LYS A 694 NZ REMARK 470 LYS A 709 CE NZ REMARK 470 LYS A 720 CG CD CE NZ REMARK 470 GLU A 753 CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 ND1 HIS A 399 O HOH A 2085 2.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 420 53.16 -112.02 REMARK 500 PHE A 493 -3.28 77.83 REMARK 500 ALA A 538 71.56 -151.82 REMARK 500 PHE A 700 -58.96 -135.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2102 DISTANCE = 6.34 ANGSTROMS REMARK 525 HOH A2131 DISTANCE = 5.91 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 801 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 413 O REMARK 620 2 THR A 416 O 84.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 802 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 499 NE2 REMARK 620 2 GLU A 501 OE2 93.4 REMARK 620 3 HIS A 587 NE2 83.5 79.3 REMARK 620 4 QAY A 901 N2 84.5 101.3 168.0 REMARK 620 5 QAY A 901 N1 81.6 128.3 149.2 27.2 REMARK 620 6 QAY A 901 N5 97.7 168.9 102.1 79.7 53.8 REMARK 620 7 HOH A2141 O 167.5 83.4 84.1 107.9 109.9 85.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 800 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 692 SG REMARK 620 2 CYS A 695 SG 106.3 REMARK 620 3 CYS A 715 SG 118.1 110.7 REMARK 620 4 HIS A 718 ND1 112.4 111.0 98.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 800 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE QAY A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1755 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1756 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 1757 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5FPU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN JARID1B IN COMPLEX WITH GSKJ1 REMARK 900 RELATED ID: 5FPV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH COMPOUND KDOAM20A REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUE NUMBER 0-MET FROM THE CONSTRUCT. KDM5B START WITH REMARK 999 PHE26. GGGG (101-105) FOUR GLYCINE LINKER INTRODUCED BUT REMARK 999 NO DENSITY OBSERVED FOR THESE RESIDUES. DBREF 5FPL A 26 101 UNP Q9UGL1 KDM5B_HUMAN 26 101 DBREF 5FPL A 374 772 UNP Q9UGL1 KDM5B_HUMAN 374 772 SEQADV 5FPL MET A 0 UNP Q9UGL1 EXPRESSION TAG SEQADV 5FPL GLY A 102 UNP Q9UGL1 LINKER SEQADV 5FPL GLY A 103 UNP Q9UGL1 LINKER SEQADV 5FPL GLY A 104 UNP Q9UGL1 LINKER SEQADV 5FPL GLY A 105 UNP Q9UGL1 LINKER SEQRES 1 A 480 MET PHE LEU PRO PRO PRO GLU CYS PRO VAL PHE GLU PRO SEQRES 2 A 480 SER TRP GLU GLU PHE ALA ASP PRO PHE ALA PHE ILE HIS SEQRES 3 A 480 LYS ILE ARG PRO ILE ALA GLU GLN THR GLY ILE CYS LYS SEQRES 4 A 480 VAL ARG PRO PRO PRO ASP TRP GLN PRO PRO PHE ALA CYS SEQRES 5 A 480 ASP VAL ASP LYS LEU HIS PHE THR PRO ARG ILE GLN ARG SEQRES 6 A 480 LEU ASN GLU LEU GLU ALA GLN THR ARG VAL LYS LEU GLY SEQRES 7 A 480 GLY GLY GLY ALA ARG ASP TYR THR LEU ARG THR PHE GLY SEQRES 8 A 480 GLU MET ALA ASP ALA PHE LYS SER ASP TYR PHE ASN MET SEQRES 9 A 480 PRO VAL HIS MET VAL PRO THR GLU LEU VAL GLU LYS GLU SEQRES 10 A 480 PHE TRP ARG LEU VAL SER THR ILE GLU GLU ASP VAL THR SEQRES 11 A 480 VAL GLU TYR GLY ALA ASP ILE ALA SER LYS GLU PHE GLY SEQRES 12 A 480 SER GLY PHE PRO VAL ARG ASP GLY LYS ILE LYS LEU SER SEQRES 13 A 480 PRO GLU GLU GLU GLU TYR LEU ASP SER GLY TRP ASN LEU SEQRES 14 A 480 ASN ASN MET PRO VAL MET GLU GLN SER VAL LEU ALA HIS SEQRES 15 A 480 ILE THR ALA ASP ILE CYS GLY MET LYS LEU PRO TRP LEU SEQRES 16 A 480 TYR VAL GLY MET CYS PHE SER SER PHE CYS TRP HIS ILE SEQRES 17 A 480 GLU ASP HIS TRP SER TYR SER ILE ASN TYR LEU HIS TRP SEQRES 18 A 480 GLY GLU PRO LYS THR TRP TYR GLY VAL PRO GLY TYR ALA SEQRES 19 A 480 ALA GLU GLN LEU GLU ASN VAL MET LYS LYS LEU ALA PRO SEQRES 20 A 480 LYS LEU PHE VAL SER GLN PRO ASP LEU LEU HIS GLN LEU SEQRES 21 A 480 VAL THR ILE MET ASN PRO ASN THR LEU MET THR HIS GLU SEQRES 22 A 480 VAL PRO VAL TYR ARG THR ASN GLN CYS ALA GLY GLU PHE SEQRES 23 A 480 VAL ILE THR PHE PRO ARG ALA TYR HIS SER GLY PHE ASN SEQRES 24 A 480 GLN GLY PHE ASN PHE ALA GLU ALA VAL ASN PHE CYS THR SEQRES 25 A 480 VAL ASP TRP LEU PRO LEU GLY ARG GLN CYS VAL GLU HIS SEQRES 26 A 480 TYR ARG LEU LEU HIS ARG TYR CYS VAL PHE SER HIS ASP SEQRES 27 A 480 GLU MET ILE CYS LYS MET ALA SER LYS ALA ASP VAL LEU SEQRES 28 A 480 ASP VAL VAL VAL ALA SER THR VAL GLN LYS ASP MET ALA SEQRES 29 A 480 ILE MET ILE GLU ASP GLU LYS ALA LEU ARG GLU THR VAL SEQRES 30 A 480 ARG LYS LEU GLY VAL ILE ASP SER GLU ARG MET ASP PHE SEQRES 31 A 480 GLU LEU LEU PRO ASP ASP GLU ARG GLN CYS VAL LYS CYS SEQRES 32 A 480 LYS THR THR CYS PHE MET SER ALA ILE SER CYS SER CYS SEQRES 33 A 480 LYS PRO GLY LEU LEU VAL CYS LEU HIS HIS VAL LYS GLU SEQRES 34 A 480 LEU CYS SER CYS PRO PRO TYR LYS TYR LYS LEU ARG TYR SEQRES 35 A 480 ARG TYR THR LEU ASP ASP LEU TYR PRO MET MET ASN ALA SEQRES 36 A 480 LEU LYS LEU ARG ALA GLU SER TYR ASN GLU TRP ALA LEU SEQRES 37 A 480 ASN VAL ASN GLU ALA LEU GLU ALA LYS ILE ASN LYS HET ZN A 800 1 HET MN A 801 1 HET MN A 802 1 HET QAY A 901 19 HET EDO A1755 4 HET EDO A1756 4 HET DMS A1757 4 HETNAM ZN ZINC ION HETNAM MN MANGANESE (II) ION HETNAM QAY 8-[4-(2-AZANYLETHYL)PYRAZOL-1-YL]-3H-PYRIDO[3,4- HETNAM 2 QAY D]PYRIMIDIN-4-ONE HETNAM EDO 1,2-ETHANEDIOL HETNAM DMS DIMETHYL SULFOXIDE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ZN ZN 2+ FORMUL 3 MN 2(MN 2+) FORMUL 5 QAY C12 H12 N6 O FORMUL 6 EDO 2(C2 H6 O2) FORMUL 8 DMS C2 H6 O S FORMUL 9 HOH *279(H2 O) HELIX 1 1 SER A 38 ALA A 43 1 6 HELIX 2 2 ASP A 44 GLU A 57 1 14 HELIX 3 3 LEU A 379 ASN A 395 1 17 HELIX 4 4 PRO A 397 VAL A 401 5 5 HELIX 5 5 PRO A 402 THR A 416 1 15 HELIX 6 6 SER A 431 GLY A 435 1 5 HELIX 7 7 SER A 448 TYR A 454 1 7 HELIX 8 8 ASN A 463 MET A 467 5 5 HELIX 9 9 VAL A 471 ILE A 475 5 5 HELIX 10 10 ILE A 479 LEU A 484 1 6 HELIX 11 11 GLU A 501 SER A 505 5 5 HELIX 12 12 PRO A 523 TYR A 525 5 3 HELIX 13 13 ALA A 526 ALA A 538 1 13 HELIX 14 14 PRO A 539 VAL A 543 5 5 HELIX 15 15 ASN A 557 HIS A 564 1 8 HELIX 16 16 TRP A 607 HIS A 622 1 16 HELIX 17 17 SER A 628 LYS A 639 1 12 HELIX 18 18 ALA A 640 LEU A 643 5 4 HELIX 19 19 ASP A 644 LEU A 672 1 29 HELIX 20 20 ASP A 681 LEU A 685 5 5 HELIX 21 21 PRO A 686 ARG A 690 5 5 HELIX 22 22 HIS A 718 LEU A 722 5 5 HELIX 23 23 PRO A 726 TYR A 728 5 3 HELIX 24 24 THR A 737 SER A 754 1 18 SHEET 1 AA 8 VAL A 34 PHE A 35 0 SHEET 2 AA 8 ILE A 61 VAL A 64 1 O LYS A 63 N PHE A 35 SHEET 3 AA 8 PHE A 578 THR A 581 -1 O PHE A 578 N VAL A 64 SHEET 4 AA 8 TYR A 506 GLY A 514 -1 O SER A 507 N THR A 581 SHEET 5 AA 8 ASN A 595 PHE A 602 -1 O PHE A 596 N HIS A 512 SHEET 6 AA 8 TRP A 486 GLY A 490 -1 O TRP A 486 N ALA A 599 SHEET 7 AA 8 THR A 422 ALA A 430 -1 O GLY A 426 N VAL A 489 SHEET 8 AA 8 ARG A 86 ARG A 89 -1 O ARG A 86 N TYR A 425 SHEET 1 AB 2 HIS A 82 PHE A 83 0 SHEET 2 AB 2 TYR A 377 THR A 378 -1 O TYR A 377 N PHE A 83 SHEET 1 AC 2 GLN A 96 THR A 97 0 SHEET 2 AC 2 LEU A 552 VAL A 553 -1 O VAL A 553 N GLN A 96 SHEET 1 AD 4 SER A 495 HIS A 499 0 SHEET 2 AD 4 HIS A 587 ASN A 591 -1 O HIS A 587 N HIS A 499 SHEET 3 AD 4 LYS A 517 GLY A 521 -1 O THR A 518 N PHE A 590 SHEET 4 AD 4 TYR A 569 GLN A 573 -1 O TYR A 569 N GLY A 521 SHEET 1 AE 3 ASP A 676 ARG A 679 0 SHEET 2 AE 3 TYR A 730 TYR A 734 1 O TYR A 730 N ASP A 676 SHEET 3 AE 3 SER A 702 CYS A 706 -1 O ALA A 703 N ARG A 733 SSBOND 1 CYS A 706 CYS A 723 1555 1555 2.07 SSBOND 2 CYS A 708 CYS A 725 1555 1555 2.04 LINK O LEU A 413 MN MN A 801 1555 1555 2.72 LINK O THR A 416 MN MN A 801 1555 1555 2.67 LINK NE2 HIS A 499 MN MN A 802 1555 1555 2.21 LINK OE2 GLU A 501 MN MN A 802 1555 1555 2.19 LINK NE2 HIS A 587 MN MN A 802 1555 1555 2.22 LINK SG CYS A 692 ZN ZN A 800 1555 1555 2.15 LINK SG CYS A 695 ZN ZN A 800 1555 1555 2.40 LINK SG CYS A 715 ZN ZN A 800 1555 1555 2.24 LINK ND1 HIS A 718 ZN ZN A 800 1555 1555 2.08 LINK MN MN A 802 N2 QAY A 901 1555 1555 1.99 LINK MN MN A 802 N1 QAY A 901 1555 1555 2.78 LINK MN MN A 802 N5 QAY A 901 1555 1555 2.11 LINK MN MN A 802 O HOH A2141 1555 1555 2.01 SITE 1 AC1 4 CYS A 692 CYS A 695 CYS A 715 HIS A 718 SITE 1 AC2 6 LEU A 90 ASN A 91 LEU A 413 THR A 416 SITE 2 AC2 6 GLU A 419 HOH A2058 SITE 1 AC3 5 HIS A 499 GLU A 501 HIS A 587 QAY A 901 SITE 2 AC3 5 HOH A2141 SITE 1 AC4 11 TYR A 425 ASP A 428 TYR A 488 PHE A 496 SITE 2 AC4 11 HIS A 499 GLU A 501 LYS A 517 TRP A 519 SITE 3 AC4 11 HIS A 587 MN A 802 HOH A2141 SITE 1 AC5 6 ASP A 630 CYS A 699 PHE A 700 MET A 701 SITE 2 AC5 6 SER A 702 HOH A2206 SITE 1 AC6 3 GLY A 524 HOH A2155 HOH A2279 SITE 1 AC7 6 ILE A 500 TRP A 504 ARG A 584 HIS A 617 SITE 2 AC7 6 TYR A 618 LEU A 621 CRYST1 142.910 142.910 152.100 90.00 90.00 120.00 P 65 2 2 12 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.006997 0.004040 0.000000 0.00000 SCALE2 0.000000 0.008080 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006575 0.00000